John N. Weinstein

33 papers B 2Misc 1Journal 28Unranked 2
YearRankTypeTitle / Venue / Authors
2022 J jnl
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.
Bioinform.
Huma Shehwana, Shwetha V. Kumar, James M. Melott, Mary A. Rohrdanz, Chris Wakefield, Zhenlin Ju, Doris R. Siwak, Yiling Lu, Bradley M. Broom, John N. Weinstein, Gordon B. Mills, Rehan Akbani
2019 J jnl
ElemCor: accurate data analysis and enrichment calculation for high-resolution LC-MS stable isotope labeling experiments.
BMC Bioinform.
Di Du, Lin Tan, Yumeng Wang, Bo Peng, John N. Weinstein, Fredric E. Wondisford, Xiaoyang Su, Philip L. Lorenzi
2019 J jnl
Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps.
F1000Research
Michael C. Ryan, Mark Stucky, Chris Wakefield, James M. Melott, Rehan Akbani, John N. Weinstein, Bradley M. Broom
2019 J jnl
Response envelope analysis for quantitative evaluation of drug combinations.
Bioinform.
Di Du, Chia-Hua Chang, Yumeng Wang, Pan Tong, Wai Kin Chan, Yulun Chiu, Bo Peng, Lin Tan, John N. Weinstein, Philip L. Lorenzi
2018 J jnl
SoS Notebook: an interactive multi-language data analysis environment.
Bioinform.
Bo Peng, Gao Wang, Jun Ma, Man Chong Leong, Chris Wakefield, James M. Melott, Yulun Chiu, Di Du, John N. Weinstein
2016 J jnl
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning.
Bioinform.
James M. Melott, John N. Weinstein, Bradley M. Broom
2016 J jnl
TCGASpliceSeq a compendium of alternative mRNA splicing in cancer.
Nucleic Acids Res.
Michael C. Ryan, Wing Chung Wong, Robert Brown, Rehan Akbani, Xiaoping Su, Bradley M. Broom, James M. Melott, John N. Weinstein
2015 J jnl
Development of a robust classifier for quality control of reverse-phase protein arrays.
Bioinform.
Zhenlin Ju, Wenbin Liu, Paul L. Roebuck, Doris R. Siwak, Nianxiang Zhang, Yiling Lu, Michael A. Davies, Rehan Akbani, John N. Weinstein, Gordon B. Mills, Kevin R. Coombes
2014 J jnl
PRADA: pipeline for RNA sequencing data analysis.
Bioinform.
Wandaliz Torres-García, Siyuan Zheng, Andrey Sivachenko, Rahulsimham Vegesna, Qianghu Wang, Rong Yao, Michael F. Berger, John N. Weinstein, Gad Getz, Roel G. W. Verhaak
2013 J jnl
VirusSeq: software to identify viruses and their integration sites using next-generation sequencing of human cancer tissue.
Bioinform.
Yunxin Chen, Hui Yao, Erika J. Thompson, Nizar M. Tannir, John N. Weinstein, Xiaoping Su
2012 J jnl
BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data.
Bioinform.
Ken Chen, John W. Wallis, Cyriac Kandoth, Joelle M. Kalicki-Veizer, Karen L. Mungall, Andrew J. Mungall, Steven J. M. Jones, Marco A. Marra, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, John N. Weinstein, Li Ding
2012 J jnl
PurityEst: estimating purity of human tumor samples using next-generation sequencing data.
Bioinform.
Xiaoping Su, Li Zhang, Jianping Zhang, Funda Meric-Bernstam, John N. Weinstein
2012 J jnl
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Bioinform.
Michael C. Ryan, James A. Cleland, Ryangguk Kim, Wing Chung Wong, John N. Weinstein
2011 J jnl
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis.
BMC Bioinform.
Barry Zeeberg, Hongfang Liu, Ari B. Kahn, Martin Ehler, Vinodh N. Rajapakse, Robert F. Bonner, Jacob D. Brown, Brian P. Brooks, Vladimir L. Larionov, William C. Reinhold, John N. Weinstein, Yves Pommier
2010 J jnl
Exposing the cancer genome atlas as a SPARQL endpoint.
J. Biomed. Informatics
Helena F. Deus, Diogo F. Veiga, Pablo R. Freire, John N. Weinstein, Gordon B. Mills, Jonas S. Almeida
2010 J jnl
Ontogenomic study of the relationship between number of gene splice variants and GO categorization.
Bioinform.
Ari B. Kahn, Barry Zeeberg, Michael C. Ryan, D. Curtis Jamison, David M. Rockoff, Yves Pommier, John N. Weinstein
2010 J jnl
Small-sample precision of ROC-related estimates.
Bioinform.
Blaise Hanczar, Jianping Hua, Chao Sima, John N. Weinstein, Michael L. Bittner, Edward R. Dougherty
2008 — conf
CellMiner: A Database Tool for the NCI-60 Cancer Cell Lines.
BIOCOMP
Uma T. Shankavaram, Sudhir Varma, David W. Kane, Margot Sunshine, Krishna Chary, William C. Reinhold, John N. Weinstein
2008 J jnl
SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies.
BMC Bioinform.
Michael C. Ryan, Barry Zeeberg, Natasha J. Caplen, James A. Cleland, Ari B. Kahn, Hongfang Liu, John N. Weinstein
2008 J jnl
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays.
BMC Bioinform.
Hans A. Kestler, André Müller, Johann M. Kraus, Malte Buchholz, Thomas M. Gress, Hongfang Liu, David W. Kane, Barry Zeeberg, John N. Weinstein
2007 J jnl
AffyProbeMiner: a web resource for computing or retrieving accurately redefined Affymetrix probe sets.
Bioinform.
Hongfang Liu, Barry Zeeberg, Gang Qu, Akif Günes Koru, Alessandro Ferrucci, Ari B. Kahn, Michael C. Ryan, Antej Nuhanovic, Peter J. Munson, William C. Reinhold, David W. Kane, John N. Weinstein
2007 B conf
Framework for Identifying Common Aberrations in DNA Copy Number Data.
RECOMB
Amir Ben-Dor, Doron Lipson, Anya Tsalenko, Mark Reimers, Lars O. Baumbusch, Michael T. Barrett, John N. Weinstein, Anne-Lise Børresen-Dale, Zohar Yakhini
2007 J jnl
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.
BMC Bioinform.
Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry Zeeberg, D. Curtis Jamison, John N. Weinstein
2006 J jnl
AbMiner: A bioinformatic resource on available monoclonal antibodies and corresponding gene identifiers for genomic, proteomic, and immunologic studies.
BMC Bioinform.
Sylvia M. Major, Satoshi Nishizuka, Daisaku Morita, Rick Rowland, Margot Sunshine, Uma T. Shankavaram, Frank Washburn, Daniel Asin, Hosein Kouros-Mehr, David W. Kane, John N. Weinstein
2005 J jnl
High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID).
BMC Bioinform.
Barry Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W. Kane, Mark Reimers, Robert M. Stephens, David Bryant, Stanley K. Burt, Eldad Elnekave, Danielle M. Hari, Thomas A. Wynn, Charlotte Cunningham-Rundles, Donn M. Stewart, David Nelson, John N. Weinstein
2005 J jnl
Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases.
BMC Bioinform.
Mark Reimers, John N. Weinstein
2004 J jnl
Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics.
BMC Bioinform.
Barry Zeeberg, Joseph Riss, David W. Kane, Kimberly J. Bussey, Edward Uchio, W. Marston Linehan, J. Carl Barrett, John N. Weinstein
2003 Misc conf
Development of Gene Ontology Tool for Biological Interpretation of Genomic and Proteomic Data.
AMIA
Weimin Feng, Geoffrey Wang, Barry Zeeberg, Kejiao Guo, Anthony T. Fojo, David W. Kane, William C. Reinhold, Samir Lababidi, John N. Weinstein, May D. Wang
2003 B conf
Inference of large-scale topology of gene regulation networks by neural nets.
SMC
Sohyoung Kim, John N. Weinstein, John J. Grefenstette
2001 J jnl
Comparison of a Neural Net-Based QSAR Algorithm (PCANN) with Hologram- and Multiple Linear Regression-Based QSAR Approaches: Application to 1, 4-Dihydropyridine-Based Calcium Channel Antagonists.
J. Chem. Inf. Comput. Sci.
Vellarkad N. Viswanadhan, Geoffrey A. Mueller, Subhash C. Basak, John N. Weinstein
2000 J jnl
Mining and Visualizing Large Anticancer Drug Discovery Databases.
J. Chem. Inf. Comput. Sci.
Leming M. Shi, Yi Fan, Jae K. Lee, Mark Waltham, Darren T. Andrews, Uwe Scherf, Kenneth D. Paull, John N. Weinstein
1998 J jnl
Mining the NCI Anticancer Drug Discovery Databases: Genetic Function Approximation for the QSAR Study of Anticancer Ellipticine Analogues.
J. Chem. Inf. Comput. Sci.
Leming M. Shi, Yi Fan, Timothy G. Myers, Patrick M. O'Connor, Kenneth D. Paull, Stephen H. Friend, John N. Weinstein
1997 — conf
Genetic function approximation in the molecular pharmacology of cancer.
ICNN
Leming M. Shi, Yi Fan, Timothy G. Myers, John N. Weinstein